The hotel, which is set to house single males, is in the Oswestry area and will start accepting the arrivals in December.
Shropshire Council says it has not been part of the planning for the move and says it is investigating whether there is a licensing issue in regard to the hotel becoming a house of multiple occupancy.
It says it is keen to be involved and has also said that three GP practices in Oswestry have come forward to support the men.
The council has just been notified of the decision.
In a letter to councillors, the council writes: "Although we were made aware of this hotel in advance of its 'go live' date of December 8, we did not give consent to this and have not been part of the planning.
"Although the responsibility for this contingency hotel sits firmly with Serco - councils do not receive funding - we are keen to be involved and support Serco/arrivals as much as possible to ensure this is as smooth an experience as we can make it. All arrivals need to be registered with a GP and have a health assessment and three GP practices in Oswestry have come forward to support."
With the area close to the Welsh border, Shropshire Council says it is in conversation with counterparts across the border.
"At the moment Serco are telling us that this will be a second, single male hotel with a maximum occupancy of 120 but we will not know for definite until arrival day."